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Magnesium in PDB 7pmm: Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3

Enzymatic activity of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3

All present enzymatic activity of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3:
3.6.4.13;

Protein crystallography data

The structure of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3, PDB code: 7pmm was solved by J.P.Wurm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.39 / 3.00
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 169.69, 169.69, 111.99, 90, 90, 90
R / Rfree (%) 19.7 / 22.5

Other elements in 7pmm:

The structure of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 (pdb code 7pmm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3, PDB code: 7pmm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7pmm

Go back to Magnesium Binding Sites List in 7pmm
Magnesium binding site 1 out of 2 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:63.1
occ:1.00
O A:HOH604 2.0 64.1 1.0
O A:HOH601 2.0 81.0 1.0
F2 A:BEF501 2.0 63.3 1.0
O3B A:ADP500 2.0 63.1 1.0
O A:HOH603 2.0 75.2 1.0
O A:HOH602 2.0 72.7 1.0
BE A:BEF501 3.4 63.1 1.0
PB A:ADP500 3.4 63.1 1.0
O1A A:ADP500 3.4 76.6 1.0
OD2 A:ASP153 3.5 72.6 1.0
O1B A:ADP500 3.6 63.1 1.0
OG1 A:THR54 3.8 70.3 1.0
OE2 A:GLU154 3.9 73.5 1.0
OD1 A:ASP153 3.9 74.2 1.0
CA A:GLY304 4.1 63.7 1.0
CG A:ASP153 4.1 72.7 1.0
F3 A:BEF501 4.2 65.6 1.0
O2B A:ADP500 4.2 63.1 1.0
O A:GLY304 4.4 66.5 1.0
PA A:ADP500 4.5 64.6 1.0
F1 A:BEF501 4.5 66.2 1.0
O3A A:ADP500 4.5 66.6 1.0
C A:GLY304 4.8 59.4 1.0
CB A:LYS53 4.8 59.2 1.0
O2A A:ADP500 4.8 63.1 1.0
NZ A:LYS53 4.9 60.2 1.0
N A:THR54 4.9 64.6 1.0
CD A:GLU154 5.0 71.2 1.0

Magnesium binding site 2 out of 2 in 7pmm

Go back to Magnesium Binding Sites List in 7pmm
Magnesium binding site 2 out of 2 in the Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dead-Box Helicase Dbpa in the Active Conformation Bound to A Ss/Dsrna Junction and Adp/BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:90.5
occ:1.00
O B:HOH604 2.0 85.6 1.0
O B:HOH603 2.0 97.8 1.0
F2 B:BEF501 2.0 95.3 1.0
O3B B:ADP500 2.0 90.8 1.0
O B:HOH602 2.0 96.7 1.0
O B:HOH601 2.0 101.0 1.0
PB B:ADP500 3.4 87.7 1.0
BE B:BEF501 3.4 92.7 1.0
OD2 B:ASP153 3.4 106.6 1.0
O2A B:ADP500 3.4 101.3 1.0
OG1 B:THR54 3.6 90.5 1.0
O2B B:ADP500 3.7 88.6 1.0
OD1 B:ASP153 3.9 91.0 1.0
CG B:ASP153 4.0 95.0 1.0
CA B:GLY304 4.1 92.7 1.0
OE2 B:GLU154 4.1 92.2 1.0
O B:GLY304 4.3 102.0 1.0
O1B B:ADP500 4.3 85.3 1.0
F1 B:BEF501 4.3 92.2 1.0
O3A B:ADP500 4.4 101.2 1.0
F3 B:BEF501 4.4 93.6 1.0
PA B:ADP500 4.5 85.1 1.0
CE B:LYS53 4.6 84.7 1.0
C B:GLY304 4.7 97.8 1.0
N B:THR54 4.8 85.2 1.0
CB B:LYS53 4.8 82.1 1.0
CB B:THR54 5.0 85.2 1.0

Reference:

J.P.Wurm, J.P.Wurm. N/A N/A.
Page generated: Thu Oct 3 04:42:26 2024

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